RetrogeneDB ID: retro_pabe_2165

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:126191165..126191820(-)
• Located in intron of: ENSPPYG00000013293

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DNAJB6
• Ensembl ID: ENSPPYG00000018228
• Aliases: None
• Description: dnaJ homolog subfamily B member 6 [Source:RefSeq peptide;Acc:NP_001127484]

Sequence

>retro_pabe_2165
CCCCGGCAGGCCTCATCCGAGGCCATCAAGAAGGCGTACCGCAAGCTGGCGCTCAAGTGGCACCCCGACAAAAACCCCGA
GAACAAGGAGGAAGCGGAGAGGAGATTCAAGCAAGTGGGCGAGGCCTACGAAGTGTTGTTGGACGCCAAGAAACGTGATA
TCTATGACCGCTATGGCGAGGCGGGGGTGGAGGGCGGCTGCGCAGGCGGCAGGCCCTTCGAGGACGCCTTGGAGTACGTC
TTCAGCTTCCGCGACCCGGCCGAGTTCTTCAGGTAGTTCTTTGGCGGCCAGGACCCATTCTCCTTTGACCTCTTGGGAAA
CCCGCTGGAGAATATTTTTGGGGGTCAGAGGAACTGCTGGGGAAGCAGAAGCAGAGCGTCTGCACCCCTTTTCTCTGCCT
TCAGTGAATTTCCAGCTTTCGGGGGTGGTTTTTCTTCTTTTGATACAGGATTTTGTTCCTTTGGCTCCCTGGGAGGTGGG
GGCCTTTCTTCCTTCTGCATGTCCTATGGTAGTGATGGGACAGGCAGCTTCAAGTCCATGTCGACTTCCACTGAAATAGT
TGATGGCAAAAAGTCACCACCAAGAGAATCATTGAGAACGGCAAGAAAGGGTGGAAGCAGAGGAAGATGGAGAGTTGAGT
AAAGTCCTTCCTAAT

Alignment

ORF - retro_pabe_2165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.61 %
• Parental protein coverage: 62.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLRPATGRFRPRYRKLALKWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGKEGLNGGGGGG
          P...........YRKLALKWHPDKNPENKEEAER.FKQV.EAYEVL.DAKKRDIYD.YG..G..GG..GG
Retrocopy PRQASSEAIKKAYRKLALKWHPDKNPENKEEAERRFKQVGEAYEVLLDAKKRDIYDRYGEAGVEGGCAGG

Parental  SHFDSPFEFGFTFRNPDDVFREFFGGRDPFSFDFFEDPFEDFFGNRRGPRGSRSRGTGSFFSAFSGFPSF
          ..F....E..F.FR.P...FR.FFGG.DPFSFD....P.E..FG..R...GSRSR.....FSAFS.FP.F
Retrocopy RPFEDALEYVFSFRDPAEFFR*FFGGQDPFSFDLLGNPLENIFGGQRNCWGSRSRASAPLFSAFSEFPAF

Parental  GSGFSSFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTKMVNGR-KITTKRIVENG-QERVEV
          G.GFSSFDTGF.SFGSLG.GGL.SF...S.G..G.G.FKS.STST..V.G..K.TTKRI.ENG.QERVE.
Retrocopy GGGFSSFDTGFCSFGSLGGGGLSSF-CMSYGSDGTGSFKSMSTSTEIVDGK<KVTTKRIIENG<QERVEA

Parental  EEDGQLKSLTIN
          EEDG.L.....N
Retrocopy EEDGELSKVLPN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	72.38 RPM
SRP007412_cerebellum	0.00 RPM	57.40 RPM
SRP007412_heart	0.00 RPM	39.38 RPM
SRP007412_kidney	0.33 RPM	38.38 RPM
SRP007412_liver	0.09 RPM	23.23 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2165 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2165 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2400
Gorilla gorilla	retro_ggor_1819
Canis familiaris	retro_cfam_8
Equus caballus	retro_ecab_105

---

Parental genes homology:

Parental genes homology involve 28 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001332	3 retrocopies	retro_amel_127, retro_amel_685, retro_amel_95,
Bos taurus	ENSBTAG00000000771	3 retrocopies	retro_btau_163, retro_btau_222, retro_btau_248,
Canis familiaris	ENSCAFG00000005174	6 retrocopies	retro_cfam_155, retro_cfam_201, retro_cfam_2085, retro_cfam_2131, retro_cfam_527, retro_cfam_8,
Callithrix jacchus	ENSCJAG00000005288	7 retrocopies	retro_cjac_104, retro_cjac_1455, retro_cjac_1648, retro_cjac_1692, retro_cjac_2922, retro_cjac_3880, retro_cjac_948,
Cavia porcellus	ENSCPOG00000013953	17 retrocopies	retro_cpor_1035, retro_cpor_1074, retro_cpor_1147, retro_cpor_1352, retro_cpor_1360, retro_cpor_1364, retro_cpor_259, retro_cpor_325, retro_cpor_38, retro_cpor_40, retro_cpor_538, retro_cpor_610, retro_cpor_720, retro_cpor_793, retro_cpor_814, retro_cpor_840, retro_cpor_952,
Equus caballus	ENSECAG00000009005	2 retrocopies	retro_ecab_105, retro_ecab_22,
Felis catus	ENSFCAG00000015654	2 retrocopies	retro_fcat_1072, retro_fcat_91,
Homo sapiens	ENSG00000105993	9 retrocopies	retro_hsap_103, retro_hsap_166, retro_hsap_2399, retro_hsap_2400, retro_hsap_4031, retro_hsap_519, retro_hsap_54, retro_hsap_889, retro_hsap_939,
Gorilla gorilla	ENSGGOG00000004703	6 retrocopies	retro_ggor_1819, retro_ggor_201, retro_ggor_210, retro_ggor_251, retro_ggor_478, retro_ggor_719,
Loxodonta africana	ENSLAFG00000013384	4 retrocopies	retro_lafr_105, retro_lafr_107, retro_lafr_260, retro_lafr_468,
Microcebus murinus	ENSMICG00000009760	1 retrocopy	retro_mmur_474,
Myotis lucifugus	ENSMLUG00000009123	4 retrocopies	retro_mluc_1371, retro_mluc_147, retro_mluc_304, retro_mluc_333,
Macaca mulatta	ENSMMUG00000003176	6 retrocopies	retro_mmul_1050, retro_mmul_165, retro_mmul_2326, retro_mmul_243, retro_mmul_379, retro_mmul_970,
Mustela putorius furo	ENSMPUG00000009797	4 retrocopies	retro_mputfur_1084, retro_mputfur_11, retro_mputfur_1199, retro_mputfur_70,
Mus musculus	ENSMUSG00000029131	6 retrocopies	retro_mmus_113, retro_mmus_171, retro_mmus_2023, retro_mmus_3273, retro_mmus_435, retro_mmus_870,
Nomascus leucogenys	ENSNLEG00000001380	5 retrocopies	retro_nleu_1524, retro_nleu_2, retro_nleu_2063, retro_nleu_2820, retro_nleu_52,
Oryctolagus cuniculus	ENSOCUG00000000064	2 retrocopies	retro_ocun_240, retro_ocun_83,
Otolemur garnettii	ENSOGAG00000010640	2 retrocopies	retro_ogar_248, retro_ogar_3412,
Pongo abelii	ENSPPYG00000009647	1 retrocopy	retro_pabe_2136,
Pongo abelii	ENSPPYG00000011252	1 retrocopy	retro_pabe_3308,
Pongo abelii	ENSPPYG00000018228	4 retrocopies	retro_pabe_100, retro_pabe_2165 , retro_pabe_226, retro_pabe_669,
Pelodiscus sinensis	ENSPSIG00000018102	1 retrocopy	retro_psin_19,
Pteropus vampyrus	ENSPVAG00000000155	1 retrocopy	retro_pvam_24,
Rattus norvegicus	ENSRNOG00000010353	6 retrocopies	retro_rnor_1680, retro_rnor_1930, retro_rnor_212, retro_rnor_2673, retro_rnor_60, retro_rnor_641,
Ictidomys tridecemlineatus	ENSSTOG00000002964	7 retrocopies	retro_itri_1090, retro_itri_1143, retro_itri_169, retro_itri_54, retro_itri_74, retro_itri_832, retro_itri_85,
Tupaia belangeri	ENSTBEG00000009586	7 retrocopies	retro_tbel_1521, retro_tbel_1533, retro_tbel_1571, retro_tbel_1978, retro_tbel_3918, retro_tbel_4142, retro_tbel_67,
Tarsius syrichta	ENSTSYG00000005448	4 retrocopies	retro_tsyr_1358, retro_tsyr_297, retro_tsyr_360, retro_tsyr_491,
Tursiops truncatus	ENSTTRG00000013929	2 retrocopies	retro_ttru_1864, retro_ttru_637,